[Bioperl-l] [Fwd: Re: A question about iBio::Index: and its correct use]

jluis.lavin at unavarra.es jluis.lavin at unavarra.es
Thu Nov 5 11:21:57 EST 2009


Thank you very much Mark, that´s a good point :$
I guess your correction is referred to the second script, isn´t it?

If it is so, there is still a problem with the first script, it doesn´t
create the PC9.fasta.idx file, instead it creates two files named:
-PC9.fasta.idx.pag
-PC9.fasta.idx.dir

which seem to be clearly related with some kind of indexing process...but,
unless the PC9.fasta.idx file is only virtual or remains hidden, I can´t
find it anywhere...
Forgive me if I´m talking nosense...

Thank you very much again for your help ;)


El Jue, 5 de Noviembre de 2009, 17:02, Mark A. Jensen escribió:
> Hey José,
> The first thing that jumps out it the index file name. Looks
> like you create it as
> PC9.fasta.idx
> But you read it as
> PC9.fasta
> Not an unusual mistake. Do
> my $inx = Bio::Index::Fasta->new('PC9.fasta.idx');
> and see if it works.
> MAJ
> ----- Original Message -----
> From: <jluis.lavin at unavarra.es>
> To: <bioperl-l at lists.open-bio.org>
> Sent: Thursday, November 05, 2009 10:46 AM
> Subject: [Bioperl-l] [Fwd: Re: A question about iBio::Index: and its
> correct
> use]
>
>
>
>
> ---------------------------- Mensaje original ----------------------------
> Subject: Re: [Bioperl-l] A question about iBio::Index: and its correct use
> From:    jluis.lavin at unavarra.es
> Fecha:   Jue, 5 de Noviembre de 2009, 16:46
> To:      "Mark A. Jensen" <maj at fortinbras.us>
> --------------------------------------------------------------------------
>
> Hi Mark,
>
> I´ve actually got two scripts, the first one is to create the index and
> the second one is to retrieve the sequence lis from the indexed file.
>
> 1)Here is the Index creation script:
>
> #!/c:/Perl -w
> use strict;
> use Bio::Index::Fasta;
> use strict;
>
> print "Enter file for indexing: \n";
> my $Index_File_Name = <STDIN>;
> my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name.".idx",
>     -write_flag => 1);
> $inx->make_index(my $File_Name);
>
> 2)And here is the sequence retrieval script:
>
> #!/c:/Perl -w
> use Bio::Index::Fasta;
> use strict;
> #PC9.fasta is my genomic file
> my $Index_File_Name ="PC9.fasta";
> my $inx = Bio::Index::Fasta->new($Index_File_Name);
> #LCS.txt is my sequences list
> @ARGV = <lCS.txt>;
> foreach  my $id (@ARGV) {
> if ($id eq ''){
> die ("empty list")
> }
> else {
> my $seqobj = $inx->fetch($id);
> my $out = new Bio::SeqIO (-file => ">>extracted_seqs.fasta",
> -format => 'fasta');
> $out->write_seq($seqobj);
> }
> }
> exit;
> }
>
> I hope this code is not a total scum...
>
> Thanks in advance ;)
>
>
>
> El Jue, 5 de Noviembre de 2009, 16:39, Mark A. Jensen escribió:
>> José -- It looks like this is a good solution to your problem. Please
>> send
>> you
>> script so we can look at it-
>> cheers Mark
>> ----- Original Message -----
>> From: <jluis.lavin at unavarra.es>
>> To: <bioperl-l at lists.open-bio.org>
>> Sent: Thursday, November 05, 2009 10:28 AM
>> Subject: [Bioperl-l] A question about iBio::Index: and its correct use
>>
>>
>>
>> Hello to all,
>>
>> I´m trying to write a script to retrieve a list of sequences from a
>> local
>> FASTA file (for example a fasta archive where all the protein models of
>> an
>> organism are stored). This file would be used by me as some kind "local
>> database" (sorry if I mistake a few concepts...)
>> I´ve been reading the BioPerl HOWTOs and I came across the
>> Bio::Index::Fasta tool.
>> If I didn´t misunderstood what I read (which can be easy because my low
>> level on programming) this Indexing tool should do the job.
>> I wrote a couple of scripts based on the documentation i read about this
>> tool, but I don´t seem to be able to create the index file to be used
>> later (to retrieve the sequences from).
>> -First of all, I want to ask the people in this forum if the
>> Bio::Index::Fasta is the right one to chose for this tasks.
>> -Then I´ll beg you to take a look at my scripts, because I don´t seem to
>> catch the bug...
>>
>> Best wishes to you all and thanks in advance ;)
>>
>> --
>> José Luis Lavín Trueba, PhD
>>
>> Dpto. de Producción Agraria
>> Grupo de Genética y Microbiología
>> Universidad Pública de Navarra
>> 31006 Pamplona
>> Navarra
>> SPAIN
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>
>
> --
> Dr. José Luis Lavín Trueba
>
> Dpto. de Producción Agraria
> Grupo de Genética y Microbiología
> Universidad Pública de Navarra
> 31006 Pamplona
> Navarra
> SPAIN
>
>
>
> --
> Dr. José Luis Lavín Trueba
>
> Dpto. de Producción Agraria
> Grupo de Genética y Microbiología
> Universidad Pública de Navarra
> 31006 Pamplona
> Navarra
> SPAIN
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>


-- 
Dr. José Luis Lavín Trueba

Dpto. de Producción Agraria
Grupo de Genética y Microbiología
Universidad Pública de Navarra
31006 Pamplona
Navarra
SPAIN




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